Butyrivibrio hungatei sp. nov. and Pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen

Draft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615T) and Butyrivibrio fibrisolvens DSM 3071 (D1T)

Here, we report the draft genome sequences of two Butyrivibrio-type strains isolated from rumen fluid. The genome sequence of Butyrivibrio hungatei DSM 14810 was 3.3 Mb with 3,093 predicted genes, while the Butyrivibrio fibrisolvens DSM 3071 genome sequence was 4.8 Mb with 4,132 predicted genes.

The Ruminal Microbiome Alterations Associated with Diet-Induced Milk Fat Depression and Milk Fat Globule Size Reduction in Dairy Goats

The aim of this study was to evaluate the effect of conjugated linoleic acid (CLA) on milk fat globule (MFG) size and the ruminal microbiome of goats. Twenty-four mid-lactation Saanen dairy goats weighing 49 ± 4.5 kg (168 ± 27 d in milk, 1.2 ± 0.1 kg milk/d, 2-3 years old) were randomly divided into four groups-a control (CON) group, which was fed a basal diet, and three CLA supplementation groups, in which 30 g CLA (low-dose group, L-CLA), 60 g CLA (medium-dose group, M-CLA), or 90 g CLA (high-dose group, H-CLA) was added to the basal diet daily. The experiment lasted for 21 days, during which time goat milk was collected for composition and MFG size analysis. On day 21 of feeding, ruminal fluid was collected from the CON and H-CLA groups for analysis of the changes in microorganismal abundance. The results showed that CLA supplementation did not affect milk production, milk protein, or lactose content in the dairy goats (p > 0.05), but significantly reduced the milk fat content (p < 0.01) compared with the CON group. The CLA supplementation significantly decreased the D[3,2] and D[4,3] of the MFGs in a dose-dependent manner (p < 0.01). Moreover, dietary CLA inclusion increased the proportion of small-sized MFGs and decreased that of large-sized ones. The results of 16S rRNA gene sequencing showed that CLA-induced milk fat depression in dairy goats was accompanied by significant changes in the relative abundance of ruminal bacterial populations, most of which belonged to the Firmicutes and Bacteroidetes phyla. The relative abundance of Rikenellaceae_RC9_gut_group and Prevolellaceae_UCG-003 in Bacteroidetes and UCG-002, Succiniclasticum, and norank_f__norank_o__Clostridia_vadinBB60_group in Firmicutes was significantly higher in the CON group than in the H-CLA group. In contrast, the relative abundance of norank_f__UCG-011, norank_f_Eubacterium_coprostanoligenes_group, unclassified_f__Lachnospiraceae, and UCG-001 in Firmicutes and norank_f__Muribaculaceae in Bacteroidetes was significantly higher in the H-CLA group than in the CON group. Correlation analysis showed that the milk fat content was negatively correlated with the relative abundance of some bacteria, including members of Firmicutes and Bacteroidetes. Similarly, MFG size (D[3,2] and D[4,3]) was negatively correlated with several members of Firmicutes and Bacteroidetes, including Lachnospiraceae, norank_f__UCG-011, UCG-001, norank_f__Eubacterium_coprostanoligenes_group (Firmicutes), and norank_f__Muribaculaceae (Bacteroidetes), while positively correlated with the relative abundance of some members of Firmicutes and Bacteroidetes, including Mycoplasma, Succiniclasticum, norank_f__norank_o__Clostridia_vadinBB60_group, UCG-002 (Firmicutes), and Rikenellaceae_RC9_gut_group (Bacteroidetes). Overall, our data indicated that CLA treatment affected milk fat content and MFG size in dairy goats, and these effects were correlated with the relative abundance of ruminal bacterial populations. These results provide the first evidence to explain the mechanism underlying diet-induced MFG from the perspective of the ruminal microbiome in dairy goats.

Reclassification of Butyrivibrio crossotus Moore et al. 1976 (Approved Lists 1980) into a novel genus as Eshraghiella crossota gen. nov., comb. nov

The reclassification of Butyrivibrio crossotus Moore et al. 1976 (Approved Lists 1980) as Eshraghiella crossota gen. nov., comb. nov. is proposed within the family Lachnospiraceae. This reclassification is based on differences revealed through the analysis of 16S rRNA, groEL, recA, and rpoB genes, as well as genome sequences, distinguishing it from other Butyrivibrio species. Comparative analysis showed that B. crossotus exhibited digital DNA-DNA hybridization (dDDH) values of 19.40-27.20% and average nucleotide identities based on blast (ANIb) values of 67.06-67.64% with other Butyrivibrio species. These values are significantly below the species delineation thresholds (dDDH, 70%; ANIb, 95-96%), justifying the proposed reclassification. Additionally, the results of the average amino acid identity (AAI) analysis indicated that this species shares 59.22-60.17% AAI with the other species of the genus Butyrivibrio, which is below the AAI threshold (65%) for a genus boundary. In addition, biochemical and morphological characteristics also support the proposal that this species is different from other species of the genus Butyrivibrio. The type strain is ATCC 29175T (DSM 2876T=T9-40AT).

Effects of two types of Coccomyxa sp. KJ on in vitro ruminal fermentation, methane production, and the rumen microbiota

Coccomyxa sp. KJ is a unicellular green microalga that accumulates abundant lipids when cultured under nitrogen-deficient conditions (KJ1) and high nitrogen levels when cultured under nitrogen-sufficient conditions (KJ2). Considering the different characteristics between KJ1 and KJ2, they are expected to have different effects on rumen fermentation. This study aimed to determine the effects of KJ1 and KJ2 on in vitro ruminal fermentation, digestibility, CH4 production, and the ruminal microbiome as corn silage substrate condition. Five treatments were evaluated: substrate only (CON) and CON + 0.5% dry matter (DM) KJ1 (KJ1_L), 1.0% DM KJ1 (KJ1_H), 0.5% DM KJ2 (KJ2_L), and 1.0% DM KJ2 (KJ2_H). DM degradability-adjusted CH4 production was inhibited by 48.4 and 40.8% in KJ2_L and KJ2_H, respectively, compared with CON. The proportion of propionate was higher in the KJ1 treatments than the CON treatment and showed further increases in the KJ2 treatments. The abundances of Megasphaera, Succiniclasticum, Selenomonas, and Ruminobacter, which are related to propionate production, were higher in KJ2_H than in CON. The results suggested that the rumen microbiome was modified by the addition of 0.5-1.0% DM KJ1 and KJ2, resulting in increased propionate and reduced CH4 production. In particular, the KJ2 treatments inhibited ruminal CH4 production more than the KJ1 treatments. These findings provide important information for inhibiting ruminal CH4 emissions, which is essential for increasing animal productivity and sustaining livestock production under future population growth.

Moringa leaf meal exerts growth benefits in small ruminants through modulating the gastrointestinal microbiome

This study investigated the impact of feeding 17% moringa leaf meal (MLM) on the ruminal and fecal microbial composition and body weight gain (BWG) performance of lambs (Ovis aries) and kids (Capra hircus). A total of n = 28 lambs (n = 14, no-moringa, n = 14, 17% moringa) and 24 kids (n = 12, no-moringa, n = 12, 17% moringa) were involved in the experiment and body weight was recorded fortnightly. Metagenomic shotgun sequencing was performed on 28, 22, and 26 ruminal solid, liquid fraction, and fecal samples from lambs, and 23, 22, and 23 samples from kids. Moringa supplementation significantly increased BWG in lambs (21.09 ± 0.78 to 26.12 ± 0.81 kg) and kids (14.60 ± 1.29 to 18.28 ± 1.09 kg) (p-value ≤ 0.01). Microbiome analysis revealed an elevated Firmicutes:Bacteroidetes ratio in the moringa diet group. Moringa-fed animals exhibited increased microbial genera associated with volatile fatty acids (VFAs) production (Prevotella, Anaerovibrio, Lachnospiraceae, Butyrivibrio, Christensenella) and starch and fiber digesters (Proteobacteria, Ruminococcus). The increase in the bacterial genus Sharpea suggested possible methane reduction and decreased proportion of pathogens, Aliarcobacter_ID28198, Campylobacter_ID194 and Campylobacter_ID1660076 suggest health benefits. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant alterations in microbial gene pool and metabolic pathways related to carbohydrate, protein, lipid and energy metabolism, indicating potential improvements in animal health. Overall, moringa feeding showed higher energy recovery, improved growth, and potential benefits in methane reduction and reduced pathogenic bacteria.

Exploration of mobile genetic elements in the ruminal microbiome of Nellore cattle

Metagenomics has made it feasible to elucidate the intricacies of the ruminal microbiome and its role in the differentiation of animal production phenotypes of significance. The search for mobile genetic elements (MGEs) has taken on great importance, as they play a critical role in the transfer of genetic material between organisms. Furthermore, these elements serve a dual purpose by controlling populations through lytic bacteriophages, thereby maintaining ecological equilibrium and driving the evolutionary progress of host microorganisms. In this study, we aimed to identify the association between ruminal bacteria and their MGEs in Nellore cattle using physical chromosomal links through the Hi-C method. Shotgun metagenomic sequencing and the proximity ligation method ProxiMeta were used to analyze DNA, getting 1,713,111,307 bp, which gave rise to 107 metagenome-assembled genomes from rumen samples of four Nellore cows maintained on pasture. Taxonomic analysis revealed that most of the bacterial genomes belonged to the families Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae and mostly encoded pathways for central carbon and other carbohydrate metabolisms. A total of 31 associations between host bacteria and MGE were identified, including 17 links to viruses and 14 links to plasmids. Additionally, we found 12 antibiotic resistance genes. To our knowledge, this is the first study in Brazilian cattle that connect MGEs with their microbial hosts. It identifies MGEs present in the rumen of pasture-raised Nellore cattle, offering insights that could advance biotechnology for food digestion and improve ruminant performance in production systems.

Integrated analysis of gut metabolome, microbiome, and exfoliome data in an equine model of intestinal injury

BACKGROUND

The equine gastrointestinal (GI) microbiome has been described in the context of various diseases. The observed changes, however, have not been linked to host function and therefore it remains unclear how specific changes in the microbiome alter cellular and molecular pathways within the GI tract. Further, non-invasive techniques to examine the host gene expression profile of the GI mucosa have been described in horses but not evaluated in response to interventions. Therefore, the objectives of our study were to (1) profile gene expression and metabolomic changes in an equine model of non-steroidal anti-inflammatory drug (NSAID)-induced intestinal inflammation and (2) apply computational data integration methods to examine host-microbiota interactions.

METHODS

Twenty horses were randomly assigned to 1 of 2 groups (n = 10): control (placebo paste) or NSAID (phenylbutazone 4.4 mg/kg orally once daily for 9 days). Fecal samples were collected on days 0 and 10 and analyzed with respect to microbiota (16S rDNA gene sequencing), metabolomic (untargeted metabolites), and host exfoliated cell transcriptomic (exfoliome) changes. Data were analyzed and integrated using a variety of computational techniques, and underlying regulatory mechanisms were inferred from features that were commonly identified by all computational approaches.

RESULTS

Phenylbutazone induced alterations in the microbiota, metabolome, and host transcriptome. Data integration identified correlation of specific bacterial genera with expression of several genes and metabolites that were linked to oxidative stress. Concomitant microbiota and metabolite changes resulted in the initiation of endoplasmic reticulum stress and unfolded protein response within the intestinal mucosa.

CONCLUSIONS

Results of integrative analysis identified an important role for oxidative stress, and subsequent cell signaling responses, in a large animal model of GI inflammation. The computational approaches for combining non-invasive platforms for unbiased assessment of host GI responses (e.g., exfoliomics) with metabolomic and microbiota changes have broad application for the field of gastroenterology. Video Abstract.

Microbial Mechanistic Insight into the Role of Yeast-Derived Postbiotics in Improving Sow Reproductive Performance in Late Gestation and Lactation Sows

The purpose of this study is to investigate the effects of supplementing Yeast-derived postbiotics (Y-dP) to the diet of sows during late pregnancy and lactation on fecal microbiota and short-chain fatty acids (SCFA) in sows and their offspring weaned piglets, as well as the relationship between gut microbiota and SCFA, serum cytokines, and sow reproductive performance. A total of 150 sows were divided into three groups: control diet (CON), CON + Y-dP 1.25 g/kg, and CON + Y-dP 2 g/kg. The results showed that supplementing 0.125% Y-dP to the diet of sows can increase the content of isobutyric acid (IBA) in the feces of pregnant sows and reduce the content of butyric acid (BA) in the feces of weaned piglets (p < 0.05). The fecal microbiota of pregnant sows β diversity reduced and piglet fecal microbiota β diversity increased (p < 0.05). Y-dP significantly increased the abundance of Actinobacteria and Limosilactobacilli in the feces of pregnant sows (p < 0.05), as well as the abundance of Verrucomicrobiota, Bacteroidota, and Fusobacteriota in the feces of piglets (p < 0.05). The abundance of Bacteroidota in the feces of pregnant sows is positively correlated with propionic acid (PA) (r > 0.5, p < 0.05). The abundance of Prevotellaceae_NK3B31_group was positively correlated with Acetic acid (AA), PA, Valerate acid (VA), and total volatile fatty acid (TVFA) in the feces of pregnant sows (r > 0.5, p < 0.05), and Bacteroidota and Prevotellaceae_NK3B31_group were negatively correlated with the number of stillbirths (r < -0.5, p < 0.05). The abundance of Lactobacillus and Holdemanella in piglet feces was positively correlated with TVFA in feces and negatively correlated with IgA in serum (r > 0.5, p < 0.05). In conclusion, supplementing Y-dP to the diet of sows from late gestation to lactation can increase the chao1 index and α diversity of fecal microorganisms in sows during lactation, increase the abundance of Actinobacteria and Limosilactobacilli in the feces of sows during pregnancy, and increase the abundance of beneficial bacteria such as Bacteroidetes in piglet feces, thereby improving intestinal health. These findings provide a reference for the application of Y-dP in sow production and a theoretical basis for Y-dP to improve sow production performance.

Effect of olive cake supplementation on faecal microbiota profile of Holstein and Modicana dairy cattle

The present study aimed to investigate the effect of olive cake supplementation on faecal microbiota of Holstein (n = 16) and Modicana (n = 16) dairy cows. Although no difference in richness was detected, within breeds and between the two dietary treatment, the PERMANOVA analysis applied to the beta diversity allowed to discriminate samples according to breeds (p < 0.001) and treatment (p < 0.001). In Holstein cows, the olive cake supplementation led to the increase of Pseudobutyrivibrio and Christensenellaceae_R7-group genera (p < 0.05) recognized as health-promoting or associated with feed efficiency. Differently, no difference was detected between control and treated groups for Modicana suggesting a high adaptive capacity to diet changes. In addition, the higher prevalence of Firmicutes phyla in the Modicana microbiota reflected its better capacity to digest the fibrous sources. Our study supports the suitability of olive cake as a feed supplement for cows and could help validating a sustainable livestock system in the Mediterranean area, characterized by a relevant oil production and by a native breeds reared with extensive systems.

Supplementing branched-chain volatile fatty acids in dual-flow cultures varying in dietary forage and corn oil concentrations. II: Biohydrogenation and incorporation into bacterial lipids

To maintain membrane homeostasis, ruminal bacteria synthesize branched-chain fatty acids (BCFA) or their derivatives (vinyl ethers) that are recovered during methylation procedures as branched-chain aldehydes (BCALD). Many strains of cellulolytic bacteria require 1 or more branched-chain volatile fatty acid (BCVFA). Therefore, the objective of this study was to investigate BCVFA incorporation into bacterial lipids under different dietary conditions. The study was an incomplete block design with 8 continuous culture fermenters used in 4 periods with treatments (n = 4) arranged as a 2 × 2 × 2 factorial. The factors were high (HF) or low forage (LF, 67 or 33% forage, 33:67 alfalfa:orchardgrass), without or with supplemental corn oil (CO; 3% dry matter, 1.5% linoleic fatty acid), and without or with 2.15 mmol/d (5 mg/d 13C each of isovalerate, isobutyrate, and 2-methylbutyrate). After methylation of bacterial pellets collected from each fermenter's effluent, fatty acids and fatty aldehydes were separated before analysis by gas chromatography and isotope ratio mass spectrometry. Supplementation of BCVFA did not influence biohydrogenation extent. Label was only recovered in branched-chain lipids. Lower forage inclusion decreased BCFA in bacterial fatty acid profile from 9.45% with HF to 7.06% with LF and decreased BCALD in bacterial aldehyde profile from 55.4% with HF to 51.4% with LF. Supplemental CO tended to decrease iso even-chain BCFA and decreased iso even-chain BCALD in their bacterial lipid profiles. The main 18:1 isomer was cis-9 18:1, which increased (P < 0.01) by 25% from CO (data not shown). Dose recovery in bacterial lipids was 43.3% lower with LF than HF. Supplemental CO decreased recovery in the HF diet but increased recovery with LF (diet × CO interaction). Recovery from anteiso odd-chain BCFA and BCALD was the greatest; therefore, 2-methylbutyrate was the BCVFA primer most used for branched-chain lipid synthesis. Recovery in iso odd-chain fatty acids (isovalerate as primer) was greater than label recovery in iso even-chain fatty acids (isobutyrate as primer). Fatty aldehydes were less than 6% of total bacterial lipids, but 26.0% of 13C recovered in lipids were recovered in BCALD because greater than 50% of aldehydes were branched-chain. Because BCFA and BCALD are important in the function and growth of bacteria, especially cellulolytics, BCVFA supplementation can support the rumen microbial consortium, increasing fiber degradation and efficiency of microbial protein synthesis.

Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats

Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.

The phenotype and genotype of fermentative prokaryotes

Fermentation is a type of metabolism pervasive in oxygen-deprived environments. Despite its importance, we know little about the range and traits of organisms that carry out this metabolism. Our study addresses this gap with a comprehensive analysis of the phenotype and genotype of fermentative prokaryotes. We assembled a dataset with phenotypic records of 8350 organisms plus 4355 genomes and 13.6 million genes. Our analysis reveals fermentation is both widespread (in ~30% of prokaryotes) and complex (forming ~300 combinations of metabolites). Furthermore, it points to previously uncharacterized proteins involved in this metabolism. Previous studies suggest that metabolic pathways for fermentation are well understood, but metabolic models built in our study show gaps in our knowledge. This study demonstrates the complexity of fermentation while showing that there is still much to learn about this metabolism. All resources in our study can be explored by the scientific community with an online, interactive tool.

Effects of the Use of Rice Grain on Growth Performances, Blood Metabolites, Rumen Fermentation, and Rumen Microbial Community in Fattening Hanwoo Steers

This study aimed to assess the influence of rice grain in the total mixed ration (TMR) on the growth performance, blood metabolites, rumen fermentation, and rumen microbial community of fattening Hanwoo steers. Two experimental diets were prepared: (i) a TMR containing 33% dry matter (DM) corn grains (Corn TMR) and (ii) a TMR containing 33% DM rice grains (Rice TMR). Twenty-two Hanwoo steers (body weight [BW], 498 ± 32 kg; months, 17 ± 0.5) were distributed into two treatment groups in a completely randomized block design according to BW. The Rice TMR group had a higher final BW and DM intake (DMI) compared to those in the Corn TMR group (p < 0.01). However, no difference was observed in the average daily gain (ADG) and feed conversion ratio (FCR) between the two treatments. For the rumen fermentation parameters, the molar portion of butyrate in the Rice TMR was higher than in the Corn TMR (p < 0.01). Streptococcus bovis tended to be higher in the Rice TMR (p = 0.09). The results of this study suggest that using rice grain as the primary starch source in TMRs may be an alternative option for fattening Hanwoo steers.

Chordicoccus furentiruminis, gen. nov., sp. nov., a novel succinic acid producing bacterium isolated from a steer on a high grain diet

This study presents MP1D12^T (=NRRL B-67553^T=NCTC 14480^T), an isolate from the ruminal content of an Angus steer fed a high grain diet. Phenotypic and genotypic traits of the isolate were explored. MP1D12^T was found to be a strictly anaerobic, catalase-negative, oxidase-negative, coccoid bacterium that frequently grows in chains. Analysis of metabolic products as a result of carbohydrate fermentation showed succinic acid as the major organic acid produced with lactic acid and acetic acid as minor products. Phylogenetic analysis of MP1D12^T based on 16S rRNA nucleotide sequence and amino acid sequences from the whole genome presents a divergent lineage from other members in the family Lachnospiraceae. 16S rRNA sequence comparison, whole genome average nucleotide identity digital DNA-DNA hybridization and average amino acid identity results suggest that MP1D12^T represents a novel species in a novel genus within the family Lachnospiraceae. We propose the creation of the genus Chordicoccus in which MP1D12^T represents the type strain for the novel species Chordicoccus furentiruminis.

A newly developed bacteriocin like substance to replace monensin in diets of lactating ewes

The aim of the present experiment was to evaluate the effect of feeding a newly produced bacteriocin-like substance (BLS) as a replacement for monensin in the diets of lactating ewes. In Experiment 1, the effects of BLS or monensin at 0.5, 1, 1.5, and 2 g/kg diet on in vitro ruminal fermentation were compared. In Experiment 2, 30 multiparous Barki ewes were divided into three treatments in a complete randomized design for 90 days. The ewes were fed a basal diet without supplementation or supplemented with monensin or BLS at 0.5 g/kg DM diet. In Experiment 1, the highest levels of BLS and monensin decreased gas production, while all levels of additives linearly decreased methane production. In Experiment 2, BLS increased nutrient digestibility. Additives increased ruminal total and individual volatile fatty acids and decreased ruminal ammonia-N. The BLS increased serum albumin and decreased the concentrations of serum liver enzymes, while both additives increased serum glucose and decreased urea-N. Additives increased daily production of milk, while the BLS treatment increased the feed efficiency. It is concluded that dietary inclusion of BLS at 0.5 g/kg DM for lactating ewes is recommended to replace monensin.

Saccharomyces cerevisiae fermentation product improves robustness of equine gut microbiome upon stress

Introduction

Nutritional and environmental stressors can disturb the gut microbiome of horses which may ultimately decrease their health and performance. We hypothesized that supplementation with a yeast-derived postbiotic (Saccharomyces cerevisiae fermentation product-SCFP) would benefit horses undergoing an established model of stress due to prolonged transportation.

Methods

Quarter horses (n = 20) were blocked based on sex, age (22 ± 3 mo) and body weight (439 ± 3 kg) and randomized to receive either a basal diet of 60% hay and 40% concentrate (CON) or the basal diet supplemented with 21 g/d Diamond V TruEquine C (SCFP; Diamond V, Cedar Rapids, IA) for 60 days. On day 57, horses were tethered with their heads elevated 35cm above wither height for 12 h to induce mild upper respiratory tract inflammation. Fecal samples were collected at days 0, 28, and 56 before induction of stress, and at 0, 12, 24, and 72 h post-stress and subjected to DNA extraction and Nanopore shotgun metagenomics. Within sample (alpha) diversity was evaluated by fitting a linear model and between sample (beta) diversity was tested with permutational ANOVA.

Results

The SCFP stabilized alpha diversity across all time points, whereas CON horses had more fluctuation (P < 0.05) at 12, 24, and 72 h post-challenge compared to d 56. A significant difference between CON and SCFP was observed at 0 and 12 h. There was no difference in beta-diversity between SCFP and CON on d 56.

Discussion

Taken together, these observations led us to conclude that treatment with SCFP resulted in more robust and stable microbial profiles in horses after stress challenge.

Effects of Different Fiber Substrates on In Vitro Rumen Fermentation Characteristics and Rumen Microbial Community in Korean Native Goats and Hanwoo Steers

Korean native goats (Capra hircus coreanae) (KNG) and Hanwoo (Bos taurus coreanae) are indigenous breeds inhabiting Korea. This study compared the in vitro rumen fermentation characteristics, dry matter (DM) degradation, and ruminal microbial communities of Korean native goats and Hanwoo steers consuming rice hay (RH) and cotton fiber (CF). The pH, ammonia-nitrogen (NH3-N), and total volatile fatty acids (VFAs) production significantly differ (p < 0.05) across species in all incubation times. After 24 h, the pH, NH3-N, and total VFAs production were higher in Korean native goats than in Hanwoo steers. Total gas, molar proportion of propionate, and total VFAs were higher (p < 0.05) in RH than in CF for both ruminant species. DM digestibility of both substrates were higher (p < 0.05) in Hanwoo steers than in KNG. Both treatments in KNG produced higher (p < 0.01) microbial DNA copies of general bacteria than those in Hanwoo steers. Butyrivibrio fibrisolvens and Fibrobacter succinogenes had significantly higher DNA copies under RH and CF in Hanwoo steers than in Korean native goats. B. fibrisolvens, Ruminococcus albus, and Ruminococcus flavifaciens after 24 h of incubation had a higher abundance (p < 0.05) in RH than in CF. Overall results suggested that rumen bacteria had host-specific and substrate-specific action for fiber digestion and contribute to improving ruminal functions of forage utilization between ruminant species.

Influence of dietary carbohydrate profile on the dairy cow rumen meta-proteome

Diet starch and fiber contents influence the rumen microbial profile and its fermentation products, yet no information exists about the effects of these dietary carbohydrate fractions on the metabolic activity of these microbes. The objective of this experiment was to evaluate the effects of dietary carbohydrate profile changes on the rumen meta-proteome profile. Eight cannulated Holstein cows were assigned to the study as part of a 4 × 4 Latin square design with a 2 × 2 factorial treatment arrangement including four 28-d periods. Cows received 1 of 4 dietary treatments on a dry matter (DM) basis. Diets included different concentrations of rumen fermentable starch (RFS) and physically effective undigested NDF (peuNDF240) content in the diet: (1) low peuNDF240, low RFS (LNLS); (2) high peuNDF240, low RFS (HNLS); (3) low peuNDF240, high RFS (LNHS); and (4) high peuNDF240, high RFS (HNHS). Rumen fluid samples were collected from each cow on the last 2 d of each period at 3 time points (0600, 1000, and 1400 h). The microbial protein fraction was isolated, isobarically labeled, and analyzed using liquid chromatography combined with tandem mass spectrometry techniques. Product ion spectra were searched using the SEQUEST search on Proteome Discoverer 2.4 (Thermo Scientific) against 71 curated microbe-specific databases. Data were analyzed using PROC MIXED procedure in SAS 9.4 (SAS Institute Inc.). A total of 138 proteins were characterized across 26 of the searched microbial species. In total, 46 proteins were affected by treatments across 17 of the searched microbial species. Of these 46 proteins, 28 were affected by RFS content across 13 microbial species, with 20 proteins having higher abundance with higher dietary RFS and 8 proteins having higher abundance with lower dietary RFS. The majority of these proteins have roles in energetics, carbon metabolism, and protein synthesis. Examples include pyruvate, phosphate dikinase (Ruminococcus albus SY3), 30S ribosomal protein S11 (Clostridium aminophilum), and methyl-coenzyme M reductase subunit α (Methanobrevibacter ruminantium strain 35063), which had higher abundances with higher dietary RFS. Conversely, glutamate dehydrogenase (Butyrivibrio fibrisolvens) and 50S ribosomal protein L5 (Pseudobutyrivibrio ruminis) and L15 (Ruminococcus bromii) had lower abundances with higher dietary RFS content. Among the remaining 18 proteins unaffected by RFS content alone, 5 proteins were affected by peuNDF240 content, and 13 were affected by peuNDF240 × RFS interactions. Our results suggest that the RFS content of the diet may have a greater influence on rumen microbial protein abundances than dietary peuNDF240 content or peuNDF240 × RFS interactions. This research highlights that dietary carbohydrate profile changes can influence rumen microbial protein abundances. Further research is needed to fully characterize the effects of diet on the rumen meta-proteome and manipulate the various roles of rumen microbes. This will aid in designing the strategies to maximize the efficiency of nutrient use in the rumen.

Pararoseburia lenta gen. nov., sp. nov. isolated from human faeces

A strictly anaerobic, motile bacterium, designated as strain NSJ-9T, was isolated from human faeces. Cells were Gram-negative, non-spore-forming, non-pigmented, and spiral-shaped or slightly curved rods with flagella. Optimal growth in M2GSC medium was observed at 37 °C (growth range 30–45 °C) and pH 6.5–7.0 (growth range 6.5–7.5) under anaerobic conditions. Phylogenetic analysis of the 16S rRNA gene revealed that strain NSJ-9T formed a distinct phylogenetic lineage that reflects a new genus in the family Lachnospiraceae , with high levels of similarity to Roseburia hominis A2-183T (95.2 %), Roseburia cecicola ATCC 33874T (95.2 %), Pseudobutyrivibrio ruminis DSM 9787T (95.2 %), Pseudobutyrivibrio xylanivorans MZ 5T (94.8%) and Roseburia faecis M72/1T (94.4 %). Genomic similarity (average nucleotide identity and digital DNA–DNA hybridization) values between strain NSJ-9T and its phylogenetic neighbours were below 71 and 31 %, respectively, indicating that strain NSJ-9T represented a novel species. The average amino acid identity and the percentage of conserved proteins between strain NSJ-9T and other related members of the family Lachnospiraceae were below 63 and 50 %, respectively, supporting that strain NSJ-9T was a member of a new genus. The predominant cellular fatty acids of strain NSJ-9T were C16 : 0 and C17 : 0 2-OH, and major polar lipids were glycolipids. The end products of glucose fermentation were acetate, propionate, iso-butyrate, butyrate and valerate. Phylogenetic and phylogenomic lineage, pairwise determined genome identity analysis suggested that strain NSJ-9T represents a novel genus in the family Lachnospiraceae . The genome size of strain NSJ-9T is 2.56 Mbp with 44.9 mol% G+C content. Collectively, the genotypic and phenotypic differences between phylogenetic relatives suggested strain NSJ-9T represented a novel species of a new genus, for which the name Pararoseburia lenta gen. nov., sp. nov. is proposed. The type strain of Pararoseburia lenta is NSJ-9T (=CGMCC 1.32469T=KCTC 15957T).

Sodium nitrate has no detrimental effect on milk fatty acid profile and rumen bacterial population in water buffaloes

This study evaluated the influence of dietary sodium nitrate on ruminal fermentation profiles, milk production and composition, microbial populations and diversity in water buffaloes. Twenty-four female water buffaloes were randomly divided into four groups and fed with 0, 0.11, 0.22, 044 g sodium nitrate per kg body weight diets, respectively. Results showed that the concentration of acetate, propionate, butyrate and total VFA in all sodium nitrate–adapted water buffaloes were greater than the control group (P  < 0.05). Although the milk fatty acids value at 0.11 g sodium nitrate/kg/d were slightly lower than other treatments, no significant differences were observed among different treatments (P  > 0.05). Compared to the control group, the archaea richness (ace and chao1) and diversity (Shannon index) indices were increased by nitrate supplementation (P  < 0.05). Compared with the control group, sodium nitrate did not affect bacterial abundance at the phylum and genus level, but the relative abundance of the methanogen genera was greatly changed. There was a tendency for Methanobrevibacter to decrease in the sodium nitrate group (P  = 0.091). Comparisons of archaea communities by PCoA analysis showed significant separation between the control group and nitrate treatments (P  = 0.025). It was concluded that added 0.11–0.44 g sodium nitrate/kg of body weight increased the rumen VFA production and archaeal diversity of water buffaloes but had no detrimental effect on milk yield or composition, fatty acids profile, rumen methanogen or Butyrivibrio group population related to biohydrogenation.

Dietary supplementation with inulin improves lactation performance and serum lipids by regulating the rumen microbiome and metabolome in dairy cows

This study investigated the effects of inulin on rumen fermentation parameters, ruminal microbiome and metabolites, as well as lactation performance and serum indexes in dairy cows. Sixteen Holstein dairy cows with similar body conditions were randomly divided into 2 groups (n = 8 per group), with inulin addition at 0 and 200 g/d per cow. The experiment lasted for 6 weeks, including a 1-week adaptation period and a 5-week treatment period. At the end of the experimental period, the milk, serum and rumen fluid were sampled and analyzed. The microbiome and metabolome in the rumen fluid were analyzed via 16S rRNA sequencing and untargeted metabolomics, respectively. The results showed that supplementation with inulin (200 g/d per cow) increased the milk yield (P = 0.001), milk protein (P = 0.032), lactose rate (P = 0.004) and proportion of saturated fatty acids (SFA) in milk (P < 0.001), but decreased the proportion of unsaturated fatty acids (USFA) (P = 0.041). Rumen pH (P = 0.040) and the concentration of NH₃–N (P = 0.024) were decreased; however, acetate (P < 0.001), propionate (P = 0.003), butyrate (P < 0.001) and lactic acid (LA) (P = 0.043) were increased. The total cholesterol (TC) (P = 0.008) and triglycerides (TG) (P = 0.01) in serum were also reduced. Additionally, inulin addition elevated the relative abundance of several beneficial symbiotic and short-chain fatty acid (SCFA)-producing bacteria, such as Muribaculaceae (false discovery rate [FDR]-adjusted P < 0.01), Acetitomaculum (FDR-adjusted P = 0.043), and Butyrivibrio (FDR-adjusted P = 0.036), while elevating the levels of L-lysine (FDR-adjusted P = 4.24 × 10⁻³), L-proline (FDR-adjusted P = 0.0158), and L-phenylalanine (FDR-adjusted P = 0.027). In contrast, several pathogens and ruminal bacteria abundant in high-fat diets, such as Escherichia-Shigella (FDR-adjusted P = 0.022), Erysipelotrichaceae__UCG-004 (FDR-adjusted P < 0.01) and RF39 (FDR-adjusted P = 0.042) were decreased along with the reduction of lysophosphatidylcholine (LysoPC) (18:1 (9Z)) (FDR-adjusted P = 1.03 × 10⁻³), LysoPC (16:0) (FDR-adjusted P = 0.0108), LysoPC (18:2 (9Z, 12Z)) (FDR-adjusted P = 1.65 × 10⁻³) and 8-methylnonenoate. In conclusion, dietary inulin supplementation could increase the relative abundance of commensal microbiota and SCFA-producing bacteria, upregulate amino acidmetabolism and downregulate lipid metabolism in the rumen of dairy cows, which might further improve lactation performance and the level of serum lipids.

Profiles of Odd- and Branched-Chain Fatty Acids and Their Correlations With Rumen Fermentation Parameters, Microbial Protein Synthesis, and Bacterial Populations Based on Pure Carbohydrate Incubation in vitro

The objectives of this study were to evaluate changes in profiles of odd- and branched-chain fatty acids (OBCFA), including pentadecanoic acid (C15:0), 13-methyltetradecanoic acid (iso-C15:0), 12-methyltetradecanoic acid (anteiso-C15:0), 14-methylpentadecanoic acid (iso-C16:0), heptadecanoic acid (C17:0), 15-methylhexadecanoic acid (iso-C17:0), and 14-methylhexadecanoic acid (anteiso-C17:0) during in vitro fermentation of pure carbohydrates mixtures in the buffer-rumen fluid. The second objective was to correlate the changes in the OBCFA profile to the corresponding changes in ruminal fermentation parameters, microbial crude protein (MCP) synthesis, and bacterial populations. Five pure carbohydrates mixtures containing different cellulose: starch (C:S) ratios, i.e., 0:100, 25:75, 50:50, 75:25, and 100:0, were incubated for 6, 12, 18, and 24 h in vitro. The results showed that there was significant interaction (P < 0.05) between C:S and incubation time for changes in all OBCFA profiles, except iso-C17:0. The highest concentration of total OBCFA (3.94 mg/g dry matter; DM) was observed in the residues after 24 h of fermentation when the C:S was 0:100, while the lowest concentration of OBCFA (1.65 mg/g DM) was produced after 6 h of incubation when the C:S was 50:50. The correlation analysis revealed that the concentration of iso-C16:0 might be a potential marker for the estimation of total volatile fatty acids (ρ = 0.78) and MCP synthesis (ρ = 0.82) in the rumen. Compared to starch degrading bacteria, cellulolytic bacteria had stronger correlations with OBCFA concentrations, and the strongest correlation was found between the population of Ruminococcus flavefaciens with C15:0 concentration (ρ = 0.70). Notably, this is the first paper reporting relationship between OBCFA with rumen fermentation products and microbial protein synthesis based on fermentation of pure carbohydrates mixtures in vitro, and thus avoid confounding interference from dietary protein and fat presence in the in vivo studies. However, more in-depth experiments are needed to substantiate the current findings.

Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms

Butyrivibrio and Pseudobutyrivibrio dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting dietary energy. Within these genera, five rumen species have been classified (Butyrivibrio fibrisolvens, Butyrivibrio hungatei, Butyrivibrio proteoclasticus, Pseudobutyrivibrio ruminis and Pseudobutyrivibrio xylanivorans) and more recently an additional Butyrivibrio sp. group was added. Given the recent increase in available genomes, we re-investigated the phylogenetic systematics and evolution of Butyrivibrio and Pseudobutyrivibrio. Across 71 genomes, we show using 16S rDNA and 40 gene marker phylogenetic trees that the current six species designations (P. ruminis, P. xylanivorans, B. fibrisolvens, Butyrivibrio sp., B. hungatei and B. proteclasticus) are found. However, pangenome analysis showed vast genomic variation and a high abundance of accessory genes (91.50–99.34 %), compared with core genes (0.66–8.50 %), within these six taxonomic groups, suggesting incorrectly assigned taxonomy. Subsequent pangenome accessory genomes under varying core gene cut-offs (%) and average nucleotide identity (ANI) analysis suggest the existence of 42 species within 32 genera. Pangenome analysis of those that still group within B. fibrisolvens, B. hungatei and P. ruminis, based on revised ANI phylogeny, also showed possession of very open genomes, illustrating the diversity that exists even within these groups. All strains of both Butyrivibrio and Pseudobutyrivibrio also shared a broad range of clusters of orthologous genes (COGs) (870), indicating recent evolution from a common ancestor. We also demonstrate that the carbohydrate-active enzymes (CAZymes) predominantly belong to glycosyl hydrolase (GH)2, 3, 5, 13 and 43, with numerous within family isoforms apparent, likely facilitating metabolic plasticity and resilience under dietary perturbations. This study provides a major advancement in our functional and evolutionary understanding of these important anaerobic bacteria.

Rumen Bacterial Community of Grazing Lactating Yaks (Poephagus grunniens) Supplemented with Concentrate Feed and/or Rumen-Protected Lysine and Methionine

Simple Summary

Ruminal microorganisms, especially bacteria, play a vital role in utilizing fibrous material in ruminants. The yak is a bovid on the Qinghai-Tibet Plateau that traditionally only grazes natural pasture all year. During lactation, energy intake of yaks is often well below requirements, and yaks lose body weight. Today, to mitigate body weight losses during lactation, suckling yaks are often offered supplementary feed. This study examined the effect of dietary supplements on rumen bacteria in lactating yak. The yaks were offered supplementary concentrate feed (C), rumen-protected Lys and Met (RPA), or both (RPA+C). The ratio of the relative abundance of Firmicutes to Bacteroidetes in RPA+C was greater than in the RPA group, while there was no difference between C and RPA+C. The intakes of supplements resulted in a number of alterations in the abundances of bacteria at the genus level. When supplemented with C, yaks increased the concentration of ruminal total volatile fatty acids (VFAs), acetate, and butyrate. These results demonstrate that supplementary feed: (1) alters the composition of rumen microbiota and VFAs of lactating yaks; and (2) can be used to manipulate the composition of rumen microbiota.

Abstract

Traditionally, yaks graze only natural pasture all year round without supplements. Forage intake of lactating yaks is below energy and protein requirements, even in the summer, and suckling yaks lose a substantial amount of significant body weight. Today, to mitigate the loss in body weight, supplementary feed is being offered to lactating yaks. However, the effects of supplementary feed on ruminal bacterial communities in lactating yaks is unknown. In the current study, we examined the effect of supplementary feed on ruminal microbiota, using 16S rRNA sequencing, and on volatile fatty acids (VFAs). Twenty-four lactating yaks of similar body weight (218 ± 19.5 kg) and grazing natural pasture were divided randomly into four groups and received different supplements: (1) rumen-protected amino acids (RPA); (2) concentrate feed (C); (3) RPA plus C (RPA+C); and (4) no supplements (control-CON). The concentrations of total VFAs, acetate, and butyrate were greater (p < 0.05) when supplemented with concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA). Bacteroidetes (B) and Firmicutes (F) were the dominant ruminal bacterial phyla in all groups. The ratio of relative abundance of F:B in RPA+C was greater than in the RPA group, while there was no difference between CON and RPC (interaction, p = 0.026). At the genus level, the relative abundances of Absconditabacteriales_SR1, Bacteroidales-RF16-group, Bacteroidales_BS11_gut_group, Prevotellaceae, and Rikenellaceae_RC9_gut_group were lesser (p < 0.05) with supplementary concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA), whereas Butyrivibrio_2 and Pseudobutyrivibrio were greater (p < 0.05) with supplementary rumen-protected amino acids (RPA and RPA+C) than without rumen-protected amino acids (CON and C). These results demonstrate that supplementary feed: (1) alters the composition of rumen microbiota and concentrations of ruminal VFAs in lactating yaks; and (2) can be used to manipulate the composition of rumen microbiota.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. III: Relation with solid passage rate and pH on prokaryotic fatty acid profile and community in continuous culture

Our objectives were to evaluate potential interactions in culture conditions that influence how exogenously dosed branched-chain VFA (BCVFA) would be recovered as elongated fatty acids (FA) or would affect bacterial populations. A 2 × 2 × 2 factorial arrangement of treatments evaluated 3 factors: (1) without versus with BCVFA (0 vs. 2 mmol/d each of isobutyrate, isovalerate, and 2-methylbutyrate; each dose was partially substituted with ¹³C-enriched tracers before and during the collection period); (2) high versus low pH (ranging diurnally from 6.3 to 6.8 vs. 5.7 to 6.2); and (3) low versus high particulate-phase passage rate (k_p; 2.5 vs. 5.0%/h) in continuous cultures administered a 50:50 forage:concentrate diet twice daily. Samples of effluent were collected and composited before harvesting bacteria from which FA and DNA were extracted. Profiles and enrichments of FA in bacteria were evaluated by gas chromatography and isotope-ratio mass spectrometry. The ¹³C enrichment in bacterial FA was calculated as percentage recovery of dosed ¹³C-labeled BCVFA. Dosing BCVFA increased the even-chain iso-FA, preventing the reduced concentration at higher k_p and potentially as a physiological response to decreased pH. However, decreasing pH decreased recovery of ¹³C in these even-chain FA, suggesting greater reliance on isobutyrate produced from degradation of dietary valine. The iso-FA were decreased, whereas anteiso-FA and 16:0 increased with decreasing pH. Thus, 2-methylbutyrate still appeared to be important as a precursor for anteiso-FA to counter the increased rigidity of bacterial membranes that had more saturated straight-chain FA when pH decreased. Provision of BCVFA stimulated the relative sequence abundance of Fibrobacter and Treponema, both of which require isobutyrate and 2-methylbutyrate. Numerous bacterial community members were shifted by low pH, including increased Prevotella and genera within the phylum Proteobacteria, at the expense of members within phylum Firmicutes. Because of relatively few interactions with pH and k_p, supplementation of BCVFA can stimulate neutral detergent fiber degradability via key fibrolytic bacteria across a range of conditions. Decreasing pH shifted bacterial populations and their FA composition, suggesting that further research is needed to distinguish pH from dietary changes.

Complete Genome Sequence of the Polysaccharide-Degrading Rumen Bacterium Pseudobutyrivibrio xylanivorans MA3014 Reveals an Incomplete Glycolytic Pathway

Bacterial species belonging to the genus Pseudobutyrivibrio are important members of the rumen microbiome contributing to the degradation of complex plant polysaccharides. Pseudobutyrivibrio xylanivorans MA3014 was selected for genome sequencing to examine its ability to breakdown and utilize plant polysaccharides. The complete genome sequence of MA3014 is 3.58 Mb, consists of three replicons (a chromosome, chromid, and plasmid), has an overall G + C content of 39.6%, and encodes 3,265 putative protein-coding genes (CDS). Comparative pan-genomic analysis of all cultivated and currently available P. xylanivorans genomes has revealed a strong correlation of orthologous genes within this rumen bacterial species. MA3014 is metabolically versatile and capable of growing on a range of simple mono- or oligosaccharides derived from complex plant polysaccharides such as pectins, mannans, starch, and hemicelluloses, with lactate, butyrate, and formate as the principal fermentation end products. The genes encoding these metabolic pathways have been identified and MA3014 is predicted to encode an extensive range of Carbohydrate-Active enZYmes with 78 glycoside hydrolases, 13 carbohydrate esterases, and 54 glycosyl transferases, suggesting an important role in solubilization of plant matter in the rumen.

Contribution of Gut Microbiota to Immunological Changes in Alzheimer's Disease

Emerging evidence suggests that both central and peripheral immunological processes play an important role in the pathogenesis of Alzheimer's disease (AD), but regulatory mechanisms remain unknown. The gut microbiota and its key metabolites are known to affect neuroinflammation by modulating the activity of peripheral and brain-resident immune cells, yet an overview on how the gut microbiota contribute to immunological alterations in AD is lacking. In this review, we discuss current literature on microbiota composition in AD patients and relevant animal models. Next, we highlight how microbiota and their metabolites may contribute to peripheral and central immunological changes in AD. Finally, we offer a future perspective on the translation of these findings into clinical practice by targeting gut microbiota to modulate inflammation in AD. Since we find that gut microbiota alterations in AD can induce peripheral and central immunological changes via the release of microbial metabolites, we propose that modulating their composition may alter ongoing inflammation and could therefore be a promising future strategy to fight progression of AD.

Live Bacillus subtilis natto Promotes Rumen Fermentation by Modulating Rumen Microbiota In Vitro

Simple Summary

Although there is much research on the applications of Bacillus subtilis natto in dairy cows, the regulation of it on rumen microorganisms and the mechanisms of microbiota that affect rumen fermentation is still unclear, such as the mechanism of improving ruminal ammonia nitrogen concentration and the pathway of increasing propionic acid production. In this study, we explored the effects of live and autoclaved B. subtilis natto on rumen microbiota in vitro by 16S rRNA gene sequencing to clarify the ruminal microbial composition and diversity and their underlying mechanisms.

Abstract

Previous studies have shown that Bacillus subtilis natto affects rumen fermentation and rumen microbial community structure, which are limited to detect a few microbial abundances using traditional methods. However, the regulation of B. subtilis natto on rumen microorganisms and the mechanisms of microbiota that affect rumen fermentation is still unclear. This study explored the effects of live and autoclaved B. subtilis natto on ruminal microbial composition and diversity in vitro using 16S rRNA gene sequencing and the underlying mechanisms. Rumen fluid was collected, allocated to thirty-six bottles, and divided into three treatments: CTR, blank control group without B. subtilis natto; LBS, CTR with 10⁹ cfu of live B. subtilis natto; and ABS, CTR with 10⁹ cfu of autoclaved B. subtilis natto. The rumen fluid was collected after 0, 6, 12, and 24 h of fermentation, and pH, ammonia nitrogen (NH₃-N), microbial protein (MCP), and volatile fatty acids (VFAs) were determined. The diversity and composition of rumen microbiota were assessed by 16S rRNA gene sequencing. The results revealed LBS affected the concentrations of NH₃-N, MCP, and VFAs (p < 0.05), especially after 12 h, which might be attributed to changes in 18 genera. Whereas ABS only enhanced pH and NH₃-N concentration compared with the CTR group (p < 0.05), which might be associated with changes in six genera. Supplementation with live B. subtilis natto improved ruminal NH₃-N and propionate concentrations, indicating that live bacteria were better than autoclaved ones. This study advances our understanding of B. subtilis natto in promoting ruminal fermentation, providing a new perspective for the precise utilization of B. subtilis natto in dairy rations.

A mixture of quebracho and chestnut tannins drives butyrate-producing bacteria populations shift in the gut microbiota of weaned piglets

Weaning is a critical period for piglets, in which unbalanced gut microbiota and/or pathogen colonisation can contribute to diseases that interfere with animal performance. Tannins are natural compounds that could be used as functional ingredients to improve gut health in pig farming thanks to their antibacterial, antioxidant, and antidiarrhoeal properties. In this study, a mixture of quebracho and chestnut tannins (1.25%) was evaluated for its efficacy in reducing the negative weaning effects on piglet growth. Microbiota composition was assessed by Illumina MiSeq 16S rRNA gene sequencing of DNA extracted from stools at the end of the trial. Sequence analysis revealed an increase in the genera Shuttleworthia, Pseudobutyrivibrio, Peptococcus, Anaerostipes, and Solobacterium in the tannin-supplemented group. Conversely, this dietary intervention reduced the abundance of the genera Syntrophococcus, Atopobium, Mitsuokella, Sharpea, and Prevotella. The populations of butyrate-producing bacteria were modulated by tannin, and higher butyrate concentrations in stools were detected in the tannin-fed pigs. Co-occurrence analysis revealed that the operational taxonomic units (OTUs) belonging to the families Veillonellaceae, Lachnospiraceae, and Coriobacteriaceae occupied the central part of the network in both the control and the tannin-fed animals. Instead, in the tannin group, the OTUs belonging to the families Acidaminococcaceae, Alcaligenaceae, and Spirochaetaceae characterised its network, whereas Family XIII Incertae Sedis occupied a more central position than in the control group. Conversely, the presence of Desulfovibrionaceae characterised the network of the control group, and this family was not present in the network of the tannin group. Moreover, the prediction of metabolic pathways revealed that the gut microbiome of the tannin group possessed an enhanced potential for carbohydrate transport and metabolism, as well as a lower abundance of pathways related to cell wall/membrane/envelope biogenesis and inorganic ion transport. In conclusion, the tested tannins seem to modulate the gut microbiota, favouring groups of butyrate-producing bacteria.

Microbiome analysis reveals the alterations in gut microbiota in different intestinal segments of Yimeng black goats

Mounting evidence revealed the importance of gut microbiota in host metabolism, immunity and physiology, and health. Yimeng black goats (YBGs) mainly distributed in Shandong province of China, displayed a complicated intestinal microecosystem, but studies of its gut microbiota are still insufficient to report. Therefore, this study was performed with an objective to characterize the intestinal microbial community structure and diversity in the small intestine (duodenum, jejunum and ileum) and cecum of YBGs and investigated the variability of gut microbiota of different intestinal segments. A total of 12 intestinal samples were collected from YBGs for high-throughput sequencing analysis based on V3-V4 variable region of 16S rRNA genes. Our results revealed alterations in gut microbial composition with obvious differences in relative abundance between the different intestinal segments. Additionally, small intestine including duodenum, jejunum and ileum not only displayed higher species abundance and diversity than cecum but also showed a significant difference among the main components of gut microbiota based on the analytical results of alpha and beta diversities. At the phylum level, Firmicutes and Proteobacteria were the most preponderant phyla in all the samples regardless of intestinal sites. Moreover, the microbiota in small intestine was significantly different from cecum, which were characterized by the higher relative abundance of Butyrivibrio_2, Megasphaera, Halomonas, Delftia, Hydrogenophaga, Limnobacter, Pseudoxanthomonas, Novosphingobium, Janibacter and Erythrobacter, whereas the levels of Butyricicoccus, unidentified_Lachnospiraceae, Fusicatenibacter, Akkermansia, Ruminococcaceae_NK4A214_group and Lactobacillus were lower. Overall, this study first characterized the profile of gut microbiota composition in different intestinal sites and provide better insight into intestinal microbial community structure and diversity of YBGs.

Stability Assessment of the Rumen Bacterial and Archaeal Communities in Dairy Cows Within a Single Lactation and Its Association With Host Phenotype

Better characterization of changes in the rumen microbiota in dairy cows over the lactation period is crucial for understanding how microbial factors may potentially be interacting with host phenotypes. In the present study, we characterized the rumen bacterial and archaeal community composition of 60 lactating Holstein dairy cows (33 multiparous and 27 primiparous), sampled twice within the same lactation with a 122 days interval. Firmicutes and Bacteroidetes dominated the rumen bacterial community and showed no difference in relative abundance between samplings. Two less abundant bacterial phyla (SR1 and Proteobacteria) and an archaeal order (Methanosarcinales), on the other hand, decreased significantly from the mid-lactation to the late-lactation period. Moreover, between-sampling stability assessment of individual operational taxonomic units (OTUs), evaluated by concordance correlation coefficient (C-value) analysis, revealed the majority of the bacterial OTUs (6,187 out of 6,363) and all the 79 archaeal OTUs to be unstable over the investigated lactation period. The remaining 176 stable bacterial OTUs were mainly assigned to Prevotella, unclassified Prevotellaceae, and unclassified Bacteroidales. Milk phenotype-based screening analysis detected 32 bacterial OTUs, mainly assigned to unclassified Bacteroidetes and Lachnospiraceae, associated with milk fat percentage, and 6 OTUs, assigned to Ruminococcus and unclassified Ruminococcaceae, associated with milk protein percentage. These OTUs were only observed in the multiparous cows. None of the archaeal OTUs was observed to be associated with the investigated phenotypic parameters, including methane production. Co-occurrence analysis of the rumen bacterial and archaeal communities revealed Fibrobacter to be positively correlated with the archaeal genus vadinCA11 (Pearson r = 0.76) and unclassified Methanomassiliicoccaceae (Pearson r = 0.64); vadinCA11, on the other hand, was negatively correlated with Methanobrevibacter (Pearson r = –0.56). In conclusion, the rumen bacterial and archaeal communities of dairy cows displayed distinct stability at different taxonomic levels. Moreover, specific members of the rumen bacterial community were observed to be associated with milk phenotype parameters, however, only in multiparous cows, indicating that dairy cow parity could be one of the driving factors for host–microbe interactions.

Effects of phenylbutazone alone or in combination with a nutritional therapeutic on gastric ulcers, intestinal permeability, and fecal microbiota in horses

Background

Gastrointestinal (GI) injury and dysbiosis are adverse events associated with nonsteroidal anti‐inflammatory drug (NSAID) use in horses. Phenylbutazone has been shown to alter GI barrier function both in vitro and ex vivo, but its effects on barrier function have not been assessed in vivo. In addition, the ability of nutritional therapeutics to prevent these changes is not known.

Objective

Our objectives were to determine whether (a) phenylbutazone affected barrier function in vivo and (b) if phenylbutazone‐induced GI injury could be ameliorated by the use of a nutritional therapeutic.

Animals

Thirty healthy horses were randomly assigned to 3 groups (n = 10 per group): control, phenylbutazone, or phenylbutazone plus nutritional therapeutic.

Methods

This study was conducted as a blinded, randomized block design. All horses were managed identically throughout the study period. Samples were collected throughout the study period to monitor fecal microbiota changes and gastric ulcers before and after treatment. Quantification of the bacterial 16S rRNA gene in blood was used as a marker of intestinal permeability.

Results

Phenylbutazone increased amounts of bacterial 16S rDNA in circulation 3.02‐fold (95% confidence interval [CI], 0.1.89‐4.17), increased gastric ulceration score by a mean of 1.1 grade (P = .02), and induced specific changes in the microbiota, including loss of Pseudobutyrivibrio of family Lachnospiraceae. These changes were attenuated by nutritional treatment.

Conclusions and Clinical Importance

Collectively, these findings suggest that phenylbutazone induces GI injury, including impaired barrier function, and that nutritional treatment could attenuate these changes.

Rumen microbiome structure and metabolites activity in dairy cows with clinical and subclinical mastitis

Background

Due to the high prevalence and complex etiology, bovine mastitis (BM) is one of the most important diseases to compromise dairy cow health and milk quality. The shift in milk compositions has been widely investigated during mastitis, but recent studies suggested that gastrointestinal microorganism also has a crucial effect on the inflammation of other peripheral tissues and organs, including the mammary gland. However, research focused on the variation of rumen inner-environment during mastitis is still limited. Therefore, the ruminal microbial profiles, metabolites, and milk compositions in cows with different udder health conditions were compared in the present study. Furthermore, the correlations between udder health status and ruminal conditions were investigated. Based on the somatic cell counts (SCC), California mastitis test (CMT) parameters and clinical symptoms of mastitis, 60 lactating Holstein dairy cows with similar body conditions (excepted for the udder health condition) were randomly divided into 3 groups (n = 20 per group) including the healthy (H) group, the subclinical mastitis (SM) group and the clinical mastitis (CM) group. Lactation performance and rumen fermentation parameters were recorded. And rumen microbiota and metabolites were also analyzed via 16S rRNA amplicon sequencing and untargeted metabolomics, respectively.

Results

As the degree of mastitis increased, rumen lactic acid (LA) (P < 0.01), acetate, propionate, butyrate, valerate (P < 0.001), and total volatile fatty acids (TVFAs) (P < 0.01) concentrations were significantly decreased. In the rumen of CM cows, the significantly increased bacteria related to intestinal and oral inflammation, such as Lachnospiraceae (FDR-adjusted P = 0.039), Moraxella (FDR-adjusted P = 0.011) and Neisseriaceae (FDR-adjusted P = 0.036), etc., were accompanied by a significant increase in 12-oxo-20-dihydroxy-leukotriene B4 (FDR-adjusted P = 5.97 × 10^− 9) and 10beta-hydroxy-6beta-isobutyrylfuranoeremophilane (FDR-adjusted P = 3.88 × 10^− 10). Meanwhile, in the rumen of SM cows, the Ruminiclostridium_9 (FDR-adjusted P = 0.042) and Enterorhabdus (FDR-adjusted P = 0.043) were increased along with increasing methenamine (FDR-adjusted P = 6.95 × 10^− 6), 5-hydroxymethyl-2-furancarboxaldehyde (5-HMF) (FDR-adjusted P = 2.02 × 10^− 6) and 6-methoxymellein (FDR-adjusted P = 2.57 × 10^− 5). The short-chain fatty acids (SCFAs)-producing bacteria and probiotics in rumen, including Prevoterotoella_1 (FDR-adjusted P = 0.045) and Bifidobacterium (FDR-adjusted P = 0.035), etc., were significantly reduced, with decreasing 2-phenylbutyric acid (2-PBA) (FDR-adjusted P = 4.37 × 10^− 6).

Conclusion

The results indicated that there was a significant shift in the ruminal microflora and metabolites associated with inflammation and immune responses during CM. Moreover, in the rumen of cows affected by SM, the relative abundance of several opportunistic pathogens and the level of metabolites which could produce antibacterial compounds or had a competitive inhibitory effect were all increased.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-020-00543-1.

Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen

Background

The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen.

Method

We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage's chemical characteristics and community structure of biofilm-embedded microbiota.

Results

Rumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial diversity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen.

Conclusion

Our findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen.

Association of Moderate Beer Consumption with the Gut Microbiota and SCFA of Healthy Adults

Fermented alcoholic drinks' contribution to the gut microbiota composition is mostly unknown. However, intestinal microorganisms can use compounds present in beer. This work explored the associations between moderate consumption of beer, microbiota composition, and short chain fatty acid (SCFA) profile. Seventy eight subjects were selected from a 261 healthy adult cohort on the basis of their alcohol consumption pattern. Two groups were compared: (1) abstainers or occasional consumption (ABS) (n = 44; <1.5 alcohol g/day), and (2) beer consumption ≥70% of total alcohol (BEER) (n = 34; 200 to 600 mL 5% vol. beer/day; <15 mL 13% vol. wine/day; <15 mL 40% vol. spirits/day). Gut microbiota composition (16S rRNA gene sequencing) and SCFA concentration were analyzed in fecal samples. No differences were found in α and β diversity between groups. The relative abundance of gut bacteria showed that Clostridiaceae was lower (p = 0.009), while Blautia and Pseudobutyrivibrio were higher (p = 0.044 and p = 0.037, respectively) in BEER versus ABS. In addition, Alkaliphilus, in men, showed lower abundance in BEER than in ABS (p = 0.025). Butyric acid was higher in BEER than in ABS (p = 0.032), and correlated with Pseudobutyrivibrio abundance. In conclusion, the changes observed in a few taxa, and the higher butyric acid concentration in consumers versus non-consumers of beer, suggest a potentially beneficial effect of moderate beer consumption on intestinal health.

Feeding of bakery by-products in the replacement of grains enhanced milk performance, modulated blood metabolic profile, and lowered the risk of rumen acidosis in dairy cows

Leftover bakery by-products (BP) from bakeries and supermarkets may serve as energy-rich ingredient in ruminant diets. The aim of the present study was to evaluate the effect of the successive substitution of cereal grains by BP on dry matter (DM) intake, milk production, and metabolic health as well as ruminal pH and eating and chewing behavior of dairy cows. Twenty-four lactating Simmental cows (149 ± 22.3 d in milk, lactation number 2.63 ± 1.38, 756 ± 89.6 kg of initial body weight) were fed a total mixed ration containing a 50:50 ratio of forage to concentrate throughout the experiment (35 d). During the first week, all cows received a control diet (without BP) as a baseline (d -7 to 0). In the next 4 wk (d 1 to 28), cows were allocated to 3 groups differing in the BP concentrations of diets [0% BP (CON), 15% BP, and 30% BP on a DM basis]. The DM intake and reticuloruminal pH were continuously measured. Blood and milk samples were taken every week, but only results from the experimental period (d 21 and 28) were used for statistical analyses, whereas results from the baseline were considered covariates. Diet analyses showed that BP inclusion increased the ether extract and sugar contents, whereby starch and neutral detergent fiber decreased. Experimental data showed that feeding BP in the diet increased DM intake. Furthermore, the cows fed 30% BP produced roughly 4 kg/d more milk and energy-corrected milk than the CON cows. The milk urea nitrogen was lower in cows fed the BP. Feeding BP reduced the blood glucose and insulin concentrations, whereas nonesterified fatty acids, β-hydroxybutyrate, and cholesterol increased linearly. Cows fed 15% BP had the shortest period of time in which ruminal pH was below 5.8, in contrast to CON cows (+188 min/d). Taken together, the results suggest that the inclusion of up to 30% BP in the diets of mid-lactation dairy cows shifted the nutrient profile from a glucogenic diet to a lipogenic diet, holding the potential to enhance performance and lower the risk of subacute ruminal acidosis in dairy cows.

The effect of a diet based on rice straw co-fermented with probiotics and enzymes versus a fresh corn Stover-based diet on the rumen bacterial community and metabolites of beef cattle

Improvement of the food value of rice straw is urgently required in rice crop growing areas to mitigate pollution caused by rice straw burning and enhance the supply of high-quality forages for ruminants. The aims of the present study were to compare the effects of fresh corn Stover and rice straw co-fermented with probiotics and enzymes on rumen fermentation and establish the feasibility of increasing the rice straw content in ruminant diets and, by extension, reducing air pollution caused by burning rice straw. Twenty Simmental hybrid beef cattle were randomly allotted to two groups with ten cattle per group. They were fed diets based either on rice straw co-fermented with probiotics and enzymes or fresh corn Stover for 90 days. Rumen fluid was sampled with an esophageal tube vacuum pump device from each animal on the mornings of days 30, 60, and 90. Bacterial diversity was evaluated by sequencing the V4–V5 region of the 16S rRNA gene. Metabolomes were analyzed by gas chromatography/time-of-flight mass spectrometry (GC–TOF/MS). Compared to cattle fed fresh corn Stover, those fed rice straw co-fermented with probiotics and enzymes had higher (P < 0.05) levels of acetic acid and propionate in rumen liquid at d 60 and d 90 respectively, higher (P < 0.05) abundances of the phyla Bacteroidetes and Fibrobacteres and the genera Ruminococcus, Saccharofermentans, Pseudobutyrivibrio, Treponema, Lachnoclostridium, and Ruminobacter, and higher (P < 0.05) concentrations of metabolites involved in metabolisms of amino acid, carbohydrate, and cofactors and vitamins. Relative to fresh corn Stover, rice straw co-fermented with probiotics and enzymes resulted in higher VFA concentrations, numbers of complex carbohydrate-decomposing and H₂-utilizing bacteria, and feed energy conversion efficiency in the rumen.

Inhibition of methanogenesis by nitrate, with or without defaunation, in continuous culture

Within the rumen, nitrate can serve as an alternative sink for aqueous hydrogen [H₂(aq)] accumulating during fermentation, producing nitrite, which ideally is further reduced to ammonium but can accumulate under conditions not yet explained. Defaunation has also been associated with decreased methanogenesis in meta-analyses because protozoa contribute significantly to H₂ production. In the present study, we applied a 2 × 2 factorial treatment arrangement in a 4 × 4 Latin square design to dual-flow continuous culture fermentors (n = 4). Treatments were control without nitrate (-NO₃^-) versus with nitrate (+NO₃^-; 1.5% of diet dry matter), factorialized with normal protozoa (faunated, FAUN) versus defaunation (DEF) by decreasing the temperature moderately and changing filters over the first 4 d of incubation. We detected no main effects of DEF or interaction of faunation status with +NO₃^-. The main effect of +NO₃^- increased H₂(aq) by 11.0 µM (+117%) compared with -NO₃^-. The main effect of +NO₃^- also decreased daily CH₄ production by 8.17 mmol CH₄/d (31%) compared with -NO₃^-. Because there were no treatment effects on neutral detergent fiber digestibility, the main effect of +NO₃^- also decreased CH₄ production by 1.43 mmol of CH₄/g of neutral detergent fiber degraded compared with -NO₃^-. There were no effects of treatment on other nutrient digestibilities, N flow, or microbial N flow per gram of nutrient digested. The spike in H₂(aq) after feeding NO₃^- provides evidence that methanogenesis is inhibited by substrate access rather than concentration, regardless of defaunation, or by direct inhibition of NO₂^-. Methanogens were not decreased by defaunation, suggesting a compensatory increase in non-protozoa-associated methanogens or an insignificant contribution of protozoa-associated methanogens. Despite adaptive reduction of NO₃^- to NH₄⁺ and methane inhibition in continuous culture, practical considerations such as potential to depress dry matter intake and on-farm ration variability should be addressed before considering NO₃^- as an avenue for greater sustainability of greenhouse gas emissions in US dairy production.

Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs

Early supplementary feeding of lambs before weaning is important to meet their nutritional needs, promote the development of rumen and improve performance. To study the effect of early supplementary feeding on rumen development and the microbiota of lambs, 22 Hu lambs were randomly divided into two groups: one group was fed with milk replacer (group C), and the other group was fed with milk replacer and starter (group S). At 28 days, six lambs in each group were slaughtered, and the rumen content and tissue samples were collected for detection and analysis. The starter significantly promoted the length of rumen papilla (P = 0.03), the concentration of acetate, propionate, butyrate and total volatile fatty acids (TVFA) (P < 0.01), which were higher in group S compared with group C. Group C had a higher rumen microbial diversity than group S. The dominant bacteria in the two groups were the same (Bacteroidetes, Firmicutes and Proteobacteria); however, they differed notably at the genus level. The microbial abundance of the two groups was significantly different for 22 species. In group C, the first three dominant bacteria were Bacteroides, Porphyromonas, and Campylobacter, while in group S they were Succinivibrio, unidentified_Prevotellaceae, and unidentified_Lachnospiraceae. Spearman correlation analysis showed that some ruminal bacteria were closely related to internal environmental factors, e.g., the relative abundances of unidentified_Bacteria, Euryarchaeota, Fusobacteria, and Gracilibacteria correlated negatively with acetate, propionate, butyrate, and TVFA (P < 0.05), while the relative abundances of Firmicutes correlated positively with acetate, propionate, butyrate and TVFA (P < 0.05). Bacteroidetes correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Synergistetes correlated negatively with acetate, propionate, and butyrate (P < 0.05); Deinococcus-Thermus correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Spirochaetes correlated negatively with propionate and TVFA (P < 0.05); and Elusimicrobia correlated negatively with propionate and butyrate (P < 0.05). Actinobacteria and Verrucomicrobia correlated positively correlated with NH₃-N. In conclusion, supplementary feeding of lambs before weaning promoted the development of rumen tissue morphology and rumen microorganisms.

Effect of Alfalfa Hay and Starter Feeding Intervention on Gastrointestinal Microbial Community, Growth and Immune Performance of Yak Calves

The present study aims to evaluate the effects of different early weaning paradigms, which supplied with extra alfalfa hay, or starter feeding, or both alfalfa hay and starter feeding, along with the milk replacer, on the gastrointestinal microbial community, growth, and immune performance of yak calves. Twenty 30-day-old male yak calves were randomly assigned to four groups, including the control (CON), alfalfa hay (A), starter feeding (S), and starter plus alfalfa hay (SA) groups. The gastrointestinal microbial colonization, the gastrointestinal development and function, and the growth and immune performance of all the yak calves were separately measured. Supplementation with alfalfa and starter feeding during the pre-weaning period significantly increased body weight, body height, body length, and chest girth. The significantly improved rumen fermentation and promoted intestinal digestion-absorption function in alfalfa and starter feeding groups, including the identified significantly increased concentrations of ruminal total volatile fatty acid (VFA); the significantly increased concentrations and proportions of acetate, butyrate, and isovalerate; the increased α-amylase activities in the duodenum, jejunum, and ileum; the increased papillae length and width of rumen epithelium and rumen wall thickness; and the increased villus height and crypt depth of the duodenum, jejunum, and ileum, could all contribute to promote the growth of calves. These significant improvements on rumen fermentation and intestinal digestion-absorption function could be further attributed to the increased proliferation of starch-decomposing, and cellulose- or hemicellulose-decomposing bacteria identified in the rumen, jejunum, and ileum. Furthermore, based on the expression of intestinal inflammatory cytokines and the rumen epithelial RNA sequencing results, alfalfa supplementation reduced the occurrence of ruminal and intestinal inflammation, whereas starter feeding supplementation was mainly beneficial to the differentiation of immune cells and the improved immune function. Meanwhile, the significantly altered relative abundances of genera in the SA group, including increased relative abundance of Limnobacter, Escherichia/Shigella, and Aquabacterium in the rumen and increased relative abundance of Coprococcus, Pseudobutyrivibrio, Flavonifractor, Synergistes, and Sutterella in jejunum, were able to reduce gastrointestinal inflammation and enhance the immune function, which enhanced the immune function of the yak calves fed with alfalfa and starter feeding. Overall, milk replacer supplemented with alfalfa and starter feeding during the pre-weaning period could alter gastrointestinal microbiota and then benefit the gastrointestinal development, digestion-absorption function, growth, and immune performance of the yak calves.

Dendrobium officinale Kimura et Migo and American ginseng mixture: A Chinese herbal formulation for gut microbiota modulation

Dendrobium officinale Kimura et Migo (D. officinale) is a famous traditional Chinese medicine (TCM). A mixture of D. officinale and American ginseng has been shown to enhance cell-mediated immunity, humoral immunity, and monocyte/macrophage functions in mice. Here, the effects of a D. officinale and American ginseng mixture on the structure of gut microbial community in dogs were examined using high-throughput 16S rRNA gene amplicon sequencing. The data revealed that while the mixture did not change the diversity of gut microbial community significantly, differences among individuals were significantly reduced. Furthermore, the mixture-responsive operational taxonomic units (OTUs) exhibited a phase-dependent expression pattern. Fifty-five OTUs were found to exhibit a mixture-induced expression pattern, among which one third were short-chain fatty acid (SCFA)-producing genera and the others were probiotic genera included Lactobacillus spp., Sutterella, Alistipes, Anaerovorax, Bilophila, Coprococcus, Gordonibacter, Oscillibacter, among others. By contrast, 36% of the OTUs exhibiting a mixture-repressed expression pattern were disease-associated microorganisms, and six genera, namely Actinomyces, Escherichia/Shigella, Fusobacterium, Slackia, Streptococcus and Solobacterium, were associated with cancer. In addition, five genera were closely associated with diabetes, namely Collinsella, Rothia, Howardella, Slackia and Intestinibacter. Our results indicate that this D. officinale and American ginseng mixture may be used as a prebiotic agent to enhance SCFA-producing genera and prevent gut dysbiosis.

High rumen degradable starch decreased goat milk fat via trans-10, cis-12 conjugated linoleic acid-mediated downregulation of lipogenesis genes, particularly, INSIG1

Background

Starch is an important substance that supplies energy to ruminants. To provide sufficient energy for high-yielding dairy ruminants, they are typically fed starch-enriched diets. However, starch-enriched diets have been proven to increase the risk of milk fat depression (MFD) in dairy cows. The starch present in ruminant diets could be divided into rumen-degradable starch (RDS) and rumen escaped starch (RES) according to their different degradation sites (rumen or intestine). Goats and cows have different sensitivities to MFD. Data regarding the potential roles of RDS in milk fat synthesis in the mammary tissue of dairy goats and in regulating the occurrence of MFD are limited.

Results

Eighteen Guanzhong dairy goats (day in milk = 185 ± 12 d) with similar parity, weight, and milk yield were selected and randomly assigned to one of three groups (n = 6), which were fed an LRDS diet (Low RDS = 20.52%), MRDS diet (Medium RDS = 22.15%), or HRDS diet (High RDS = 24.88%) for 5 weeks. Compared with that of the LRDS group, the milk fat contents in the MRDS and HRDS groups significantly decreased. The yields of short-, medium- and long-chain fatty acids decreased in the HRDS group. Furthermore, increased RDS significantly decreased ruminal B. fibrisolvens and Pseudobutyrivibrio abundances and increased the trans-10, cis-12 conjugated linoleic acid (CLA) and trans-10 C18:1 contents in the rumen fluid.

A multiomics study revealed that the HRDS diet affected mammary lipid metabolism down-regulation of ACSS2, MVD, AGPS, SCD5, FADS2, CERCAM, SC5D, HSD17B7, HSD17B12, ATM, TP53RK, GDF1 and LOC102177400. Remarkably, the significant decrease of INSIG1, whose expression was depressed by trans-10, cis-12 CLA, could reduce the activity of SREBP and, consequently, downregulate the downstream gene expression of SREBF1.

Conclusions

HRDS-induced goat MFD resulted from the downregulation of genes involved in lipogenesis, particularly, INSIG1. Specifically, even though the total starch content and the concentrate-to-fiber ratio were the same as those of the high-RDS diet, the low and medium RDS diets did not cause MFD in lactating goats.

Effects of aging on the quality of roasted sesame-like flavor Daqu

Background

Daqu, the saccharification, fermentation, and aroma-producing agents for Baijiu brewing, is prepared using a complex process. Aging is important for improving the quality of Daqu, but its impact has rarely been studied. This study investigated changes in the physicochemical properties, flavor compounds, and microbial communities during aging of Daqu with a roasted sesame-like flavor.

Results

The physicochemical properties changed continuously during aging to provide a high esterifying activity. Aging removed unpleasant flavor compounds and helped to stabilize the flavor compounds in mature Daqu. A high-throughput sequencing approach was used to analyze the changing composition of the microbial communities during aging. Aging helped to modify the microbial population to produce better Baijiu by eliminating low-abundance microbial communities and optimizing the proportion of predominant microbial communities. Nine genera of prokaryotic microbes formed the core microbiota in Daqu after aging. Regarding eukaryotic microbes, Zygomycota, the predominant community, increased in the first 2 months, then decreased in the third month of aging, while Ascomycota, the subdominant community, showed the opposite behavior. Absidia, Trichocomaceae_norank and Rhizopus were the predominant genera in the mature Daqu.

Conclusions

Significant correlations between microbiota and physicochemical properties or flavor compounds were observed, indicating that optimizing microbial communities is essential for aging Daqu. This study provides detailed information on aging during Daqu preparation.

Bacillus strains improve growth performance via enhancing digestive function and anti-disease ability in young and weaning rex rabbits

Numerous studies have shown that probiotic Bacillus could promote growth and enhance anti-disease ability in animal. In present study, the mixture of three Bacillus strains, which were isolated from rex rabbits and showed high cellulose, protease, and amylase activities, was added into the diet for investigating its effects on young and weaning rex rabbits. For experiment 1, 40 young rex rabbits (9 weeks old) were randomly divided into four groups and fed with diets containing 0 (NC), 1.0 × 10⁵ cfu/g (LC), 1.0 × 10⁶ cfu/g (MC), and 1.0 × 10⁷ cfu/g (HC) Bacillus strains for 4 weeks. For experiment 2, 80 weaning rex rabbits (5 weeks old) were randomly divided into four groups and fed with diet containing 0 (control), 1.0 × 10⁵ cfu/g (T-1), 1.0 × 10⁶ cfu/g (T-2), and 1.0 × 10⁷ cfu/g (T-3) Bacillus strains for 8 weeks. The results showed that Bacillus strains at a dose of 1.0 × 10⁶ cfu/g significantly enhanced growth performance, increased immune organ indexes, improved serum biochemical parameters, and heightened antioxidant capacity. It also markedly improved the intestinal microbiota by increasing Lactobacillus spp., Bacillus spp. counts, and decreased Escherichia coli count. In addition, the Bacillus mixture raised the concentrations of acetic acid, propionic acid, and butyric acid as well as protease, amylase, and cellulase activities of young and weaning rex rabbits. Moreover, for weaning rex rabbits, the inclusion of Bacillus strains also upregulated the abundance of cellulolytic bacteria and improved intestinal morphology. Therefore, our results indicated that Bacillus strains could facilitate the growth of young and weaning rex rabbits by improving digestive function and anti-disease ability. KEY POINTS: • Bacillus with high extracellular enzyme activity were isolated from rex rabbits. • Bacillus could improve growth performance of young and weaning rex rabbits. • The digestive function of young and weaning rex rabbits could be improved by Bacillus.

Ruminal Microbiota and Fermentation in Response to Dietary Protein and Energy Levels in Weaned Lambs

Simple Summary

Ruminants, such as sheep, are economically important because they contribute to digesting and converting plant materials into edible meat and milk for humans to consume. An adequate plane of nutrients, such as energy and protein, is essential for rumen development and growth. However, sheep production is mostly affected by inadequate nutrition in rural areas of China. As one of the most prolific and perennial estrus breeds in China, Hu sheep has huge potential for catering to the growing meat demands of the market and consumers. In this study, the effects of dietary energy and protein levels on growth performance, microbial diversity, and physiological properties of the rumen in weaned lambs were evaluated. The results showed that a low dietary energy level restrained growth performance and changed the microbiota and associated ruminal fermentation phenotypes of lambs. However, protein had a minor effect. The findings are of great significance for promoting rumen development and establishing the optimal nutrient supply strategy for lambs.

Abstract

Supplying sufficient nutrients, such as dietary energy and protein, has a great effect on the growth and rumen development of ruminants. This study was conducted to evaluate the effects of dietary energy and protein levels on growth performance, microbial diversity, and structural and physiological properties of the rumen in weaned lambs. A total of 64 two-month-old Hu lambs were randomly allotted to 2 × 2 factorial arrangements with four replicates and with four lambs (half male and half female) in each replicate. The first factor was two levels of dietary metabolizable energy (ME) density (ME = 10.9 MJ/Kg or 8.6 MJ/Kg), and the second factor was two levels of dietary crude protein (CP) content (CP = 15.7% or 11.8%). The trial lasted for 60 days. A low dietary energy level restrained the growth performance of lambs (p < 0.05). The ruminal concentration of acetate and the ratio of acetate to propionate increased but the propionate concentration decreased significantly with the low energy diet. However, the rumen morphology was not affected by the diet energy and protein levels. Moreover, a low energy diet increased ruminal bacterial diversity but reduced the abundance of the phylum Proteobacteria (p < 0.05) and genus Succinivibrionaceae_uncultured (p < 0.05), which was associated with the change in ruminal fermentation phenotypes. By indicator species analysis, we found three indicator OTUs in the high energy group (Succinivibrionaceae_uncultured, Veillonellaceae_unclassified and Veillonellaceae_uncultured (p < 0.01)) and two indicator OTUs in the low energy group (Bacteroidales_norank and Lachnospiraceae_uncultured (p < 0.01)). In conclusion, these findings added new dimensions to our understanding of the diet effect on rumen microbial community and fermentation response, and are of great significance for establishing the optimal nutrient supply strategy for lambs.

Pretreatment of Lignocellulosic Biomass with Cattle Rumen Fluid for Methane Production: Fate of Added Rumen Microbes and Indigenous Microbes of Methane Seed Sludge

The pretreatment of lignocellulosic substrates with cattle rumen fluid was successfully developed to increase methane production. In the present study, a 16S rRNA gene-targeted amplicon sequencing approach using the MiSeq platform was applied to elucidate the effects of the rumen fluid treatment on the microbial community structure in laboratory-scale batch methane fermenters. Methane production in fermenters fed rumen fluid-treated rapeseed (2,077.3 mL CH4 reactor-1 for a 6-h treatment) was markedly higher than that in fermenters fed untreated rapeseed (1,325.8 mL CH4 reactor-1). Microbial community profiling showed that the relative abundance of known lignocellulose-degrading bacteria corresponded to lignocellulose-degrading enzymatic activities. Some dominant indigenous cellulolytic and hemicellulolytic bacteria in seed sludge (e.g., Cellulosilyticum lentocellum and Ruminococcus flavefaciens) and rumen fluid (e.g., Butyrivibrio fibrisolvens and Prevotella ruminicola) became undetectable or markedly decreased in abundance in the fermenters fed rumen fluid-treated rapeseed, whereas some bacteria derived from seed sludge (e.g., Ruminofilibacter xylanolyticum) and rumen fluid (e.g., R. albus) remained detectable until the completion of methane production. Thus, several lignocellulose-degrading bacteria associated with rumen fluid proliferated in the fermenters, and may play an important role in the degradation of lignocellulosic compounds in the fermenter.